Nucleic acids are vital information carriers of biology, and the detection, amplification, and identification of nucleic acids has formed the basis for a vast sector of biotechnology. In particular, methods such as the polymerase chain reaction (PCR) (Saiki et al. Science 239, 487-491 (1988)) have been used all over the world as a reliable means of amplifying DNA, while reverse transcriptase methods have been used to probe the transcriptome. The operation of DNA polymerase, RNA polymerase, and reverse transcriptase typically uses a short oligonucleotide fragment known as a primer to direct the portion of a long target to be replicated or transcribed.
Although the specificity of nucleic acid hybridization is frequently sufficient to direct enzymatic activity for most target sequences, targets with repetitive sequence, secondary structure, and high G/C content are difficult to amplify with high yield. Furthermore, high backgrounds of other nucleic acids can frequently lead to incorrect amplification, such as in the case of single copy human genome amplification. Finally, multiplexed amplification, such as from a DNA chip pool, can be difficult to achieve due to the large number of orthogonal amplification reactions that must occur simultaneously. Similar problems exist for transcription and for reverse transcription.